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SHODAN's back, and none too happy.

System Shock 2 is an interesting example of cut or changed content. The strings.crf file contains effectively the history of the game development, and it's simply a rebranded zip file housing plaintext files. The root of the archive contains all the finalized content, while the rcs folder contains historical data.

Cut/Altered Items

OBJLOOKS.STR, lines 89 and 91

Tool_p1: "The CraftTech Electron Spanner is an over-engineered device is generally found in one of two-states:
Broken or about to be broken. Essentially useless, the spanner profited TriOp well until it was
discovered that well-placed officials in the UNN were authorizing their purchase at around 4000% of
market value."
Tool_p2: "The CraftTech Welder exhibits one serious design flaw: it simply doesn't work. However, to save
political face, the unit ended up on numerous TriOp starships and installations. More or less, a paperweight."

The game features many useless objects, so why cut two cracks directed at bureaucratic waste?

OBJNAME.STR, line 145

Vacuum_suit_n83: "A vacuum suit."

There is no vacuum suit in the game. The finalized object name list does contain an entry internally known as Vacc_suit, but this is shown to the player as "A hazard suit". Likely cut when the mission to depressurize an entire deck was cut.

These are obviously chemical compounds, and doing research in-game often requires the player to find chemicals...but all the used chemicals are elements, not compounds.

(These are just a few examples, as the file is littered with them.)

OBJNAME.STR, line 234

Lead_Pipe_n20: "A sturdy lead pipe"

Likely a holdover from the original game, where the initial weapon is a lead pipe. The starter weapon here is a wrench.

Mission/Plot Changes

Deck 1 (Engineering) - LEVEL01.STR

Purging radiation
Lines 273 & 274

LogText7:"To: All Engineering Staff\n\
This ship's safety systems are a total mess. I told those idiots...In the event of total failure of the
reactant coolant systems, you leech the contaminant from the deck by a controlled rapid decompression.
You can do this by opening the shuttle bay doory. There's a control system in command control that
controls the shuttle door protocols. You can override these protocols with an systems override chip
45M/dEX. The chip's stored in auxilary storage 5 in the coolant tubes, keycode: 34760.\n"

The final game has you purge the radiation by overriding the fluidics monitoring computer, which also requires hardware override 45M/dEX.

Warning about the fuel scoop
Line 218

EmailText4:"Stop where you are...if you heat up the engine core with the Fuel Scoop open, you could flood
the catalyst chambers with reactant and incinerate the entire ship. Head down to the Fuel Scoop and set
the scoop modulation to 4523. Careful...modulating the scoop will send out a class B alert to the security
system...you might get some company.\n"

This warning is not present in the final game, and indeed there is nothing to be done with the fuel scoop.

Deck 2 (Medical/R&D) - LEVEL02.STR

No notable changes.

Deck 3 (Hydroponics) - LEVEL03.STR

Changes to research
Line 48

EmailText2:"Okay, stop where you are. There’s a vial of an experimental material called Toxin-A. I’ve
picked up some data from some of the sci staff resisting the xenomorphs. They were developing the Toxin
to reduce the growth of the aliens. But I can’t find any data on how you should use it. You must
research the toxin with the Crick analyzer. If you don’t have a Crick Analyzer, find one. If I figured
this out, they might have to. Remember... Your corpse is useless to me.\n"

There is no Crick Analyzer, and research is done through the Research skill. Since the final game just requires you to have the Research skill for this part, you are given enough cyber modules to purchase the skill if needed.

Deck 4 (Operations) - LEVEL04.STR

The sim units
Line 51

EmailText1:"My children have co-opted the simulational computers on this deck. They use that power to
conceive a mutagen that will transform the meat of your dead comrades into hunter-killer hybrids. I will
this not allow this to happen. Destroy the 4 simulational computer nodes...but beware...life grows
within the womb of these walls...life that has never seen the surface of the earth...Matters on deck 5
also require your attention. Approach your work as you see fit...but accomplish, human...disappointment
is not something I will accept from a mote such as you.\n"

While dealing with the simulation computers is still required in the final game, the number and method have both changed: the final has three computers which must be reprogrammed with associated cards.

Deck 5 (Recreation) - LEVEL05.STR

Scrapped ambush?
Line 50

EmailText1:"They lie in ambush. Hack the computer inside the security station to take control of their
defenses. Why do you delay? Obey me.\n"

This warning does not appear in the final game. Also, turrets are hacked directly rather than by way of remote computers.

The transmitter
Line 266

Okay, Delacroix. Frank and I have got the transmitter almost ready to go. Once its up and running, we’ll
be able to warn Earth. As soon as you get the access shunt online later today, we’ll be able to divert
enough power from the primary computer core to make the transmission. Until then, we’ve locked off the
gym. If something were to happen to us and you needed the access code, think back to the night at the
basketball game. You'll find the answer there.\n"

The transmitter requires a code to work, but this code is not a reference to a basketball game and no reference is made to any game while on Deck 5.

Player's origin
Line 269

LogText2:"Mon ami, there is something you should know about. I have received information from some form
of artificial intelligence that is calling itself SHODAN. Yes, SHODAN. Wherever this intelligence actually
came from, it has a terrible grudge against these annelids and has saved my life more than once. "SHODAN"
has told me that there is a deep cover UNN operative aboard the ship, armed to the hilt and equipped with
R-grade cyber implants. This individual apparently lead us to Canopus in the first place and Forrest and
Korenchkin were apparently taking their orders from him. I’ve attached a security shot of the operative
taken shortly after their revival in Cryo recovery.\n"

A very interesting change regarding the player character. While this log exists in the final game, the extent of the player's backstory is limited to being a UNN operative. This also makes reference to Forrest, a character who was ultimately renamed Diego to tie to the first game. Also, the released game takes place near Tau Ceti, not Canopus.

Deck 6 (Command) - LEVEL06.STR

No notable changes.

The Rickenbacker - LEVEL07.STR

Meson acceleration coil
Line 61

EmailText2:"t is clear that the secondary meson acceleration beyond this portal has also been
sabotaged...if you approach it, you’ll destroy the rest of this ship.\n"

Issues with the meson acceleration coil are still present in the final game, but you are warned about them far in advance to finding the door the the problem coil. There is however an entry in the final game if you attempt to enter the area where the coil resides prior to reversing gravity, but it's SHODAN berating you for being stupid.

The Many - LEVEL08.STR

No notable changes.

SKILHELP.STR

Weapon skills are mostly the same, although Alien was replaced with Exotic and Conventional was replaced by Standard. Alien Research was truncated to simply Research, while Weapon Repair, Weapon Modification, and Weapon Maintenance all dropped the prefix.

STATHELP.STR

The Psionic ability stat was originally going to be Intelligence. Likely changed when they found they had no other use for it at all.

A Luck stat is mentioned, but was completely scrapped. Similarly, experience points are referred to despite no such thing existing in the final game.

These three changes happened fairly early in development, with the EXP idea seemingly lasting the longest.

TRAITS.STR

Cyber-assimilation O/S Upgrade was originally called Borg, which was most likely changed due to copyright reasons, although the associated item that it allows you to find on destroyed robots is still referred to internally as "cheeseborger".